Polygenic Score (PGS) ID: PGS001014

Predicted Trait
Reported Trait Other disorders of pancreatic internal secretion (time-to-event)
Mapped Trait(s) pancreas disease (EFO_0009605)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC654
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_HC654
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 69
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 1,552 cases
  • , 268,152 controls
]
 European UKB — — — white British ancestry —

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM007833 PSS004585|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other disorders of pancreatic internal secretion — AUROC: 0.65665 [0.58207, 0.73122] R²: 0.03396
Incremental AUROC (full-covars): -0.00764
PGS R2 (no covariates): 0.00359
PGS AUROC (no covariates): 0.4188 [0.34373, 0.49387]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007834 PSS004586|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other disorders of pancreatic internal secretion — AUROC: 0.86357 [0.7171, 1.0] R²: 0.15881
Incremental AUROC (full-covars): -0.01283
PGS R2 (no covariates): 0.02019
PGS AUROC (no covariates): 0.35821 [0.13039, 0.58603]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007835 PSS004587|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other disorders of pancreatic internal secretion — AUROC: 0.64476 [0.60172, 0.6878] R²: 0.02426
Incremental AUROC (full-covars): -0.00192
PGS R2 (no covariates): 0.00131
PGS AUROC (no covariates): 0.52076 [0.4675, 0.57402]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007836 PSS004588|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other disorders of pancreatic internal secretion — AUROC: 0.73516 [0.68282, 0.7875] R²: 0.07572
Incremental AUROC (full-covars): -0.00172
PGS R2 (no covariates): 0.00033
PGS AUROC (no covariates): 0.50209 [0.4372, 0.56698]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007837 PSS004589|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other disorders of pancreatic internal secretion — AUROC: 0.63289 [0.60549, 0.66029] R²: 0.01894
Incremental AUROC (full-covars): 0.01617
PGS R2 (no covariates): 0.00452
PGS AUROC (no covariates): 0.55692 [0.52735, 0.58649]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS004585 — —
[
  • 64 cases
  • , 6,433 controls
]
 — African unspecified — UKB —
PSS004586 — —
[
  • 5 cases
  • , 1,699 controls
]
 — East Asian — UKB —
PSS004587 — —
[
  • 134 cases
  • , 24,771 controls
]
 — European non-white British ancestry UKB —
PSS004588 — —
[
  • 89 cases
  • , 7,742 controls
]
 — South Asian — UKB —
PSS004589 — —
[
  • 385 cases
  • , 67,040 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)